Exploring the Mechanism of Covalent Inhibition: Simulating the Binding Free Energy of α-Ketoamide Inhibitors of the Main Protease of SARS-CoV-2

Abstract

The development of reliable ways of predicting the binding free energies of covalent inhibitors is a challenge for computer-aided drug design. Such development is important, for example, in the fight against the SARS-CoV-2 virus, in which covalent inhibitors can provide a promising tool for blocking Mpro, the main protease of the virus. This work develops a reliable and practical protocol for evaluating the binding free energy of covalent inhibitors. Our protocol presents a major advance over other approaches that do not consider the chemical contribution of the binding free energy. Our strategy combines the empirical valence bond method for evaluating the reaction energy profile and the PDLD/S-LRA/β method for evaluating the noncovalent part of the binding process. This protocol has been used in the calculations of the binding free energy of an α-ketoamide inhibitor of Mpro. Encouragingly, our approach reproduces the observed binding free energy. Our study of covalent inhibitors of cysteine proteases indicates that in the choice of an effective warhead it is crucial to focus on the exothermicity of the point on the free energy surface of a peptide cleavage that connects the acylation and deacylation steps. Overall, we believe that our approach should provide a powerful and effective method for in silico design of covalent drugs.

Multiscale Simulations of SARS-CoV-2 3CL Protease Inhibition with Aldehyde Derivatives. Role of Protein and Inhibitor Conformational Changes in the Reaction Mechanism

“…Starting from the E–I complex, the free-energy cost of forming the IP is 9.3 kcal·mol –1 , a value slightly larger than that obtained when a peptide substrate is present in the active site (4.8 kcal·mol –1 ). 16 The value obtained for 11a is similar to those found for the formation of the IP under the presence of other inhibitors: 7.3 kcal·mol –1 with an α-ketoamide inhibitor 20 and 10.3 with a Michael acceptor. 18 These values are systematically larger than the free-energy cost evaluated for the apo enzyme, which was found to be 2.9 kcal·mol –1 in two different studies, 16 , 20 indicating that desolvation of the active site upon ligand binding can destabilize the IP form.…”

“… 16 , 17 Regarding covalent inhibition, QM/MM methods have been also used to analyze the reaction with irreversible Michael acceptors 18 , 19 and α-ketoamide inhibitors. 20 This last study provides a complete evaluation of the binding free energy of the covalent inhibitor as the sum of the noncovalent binding and the reaction steps. In this work, we use classical and hybrid QM/MM molecular dynamics simulations to explore the inactivation mechanism of SARS-CoV-2 3CL protease by an aldehyde derivative, 11a .…”

Benchmark of Popular Free Energy Approaches Revealing the Inhibitors Binding to SARS-CoV-2 Mpro

“… 87 The further expensive computing approach such as QM/MM or PDLD/S-LRA/β should be thus carried out to refine the binding process. 87 − 89 However, in this work, the computational investigations were limited in the framework of the classical simulation, which is widely used and good enough to estimate the potential inhibitors for Mpro. Moreover, in average over complexes, the Δ G FEP value is −9.87 ± 1.20 kcal mol –1 , which overestimates ca.…”

Multiscale Simulations of SARS-CoV-2 3CL Protease Inhibition with Aldehyde Derivatives. Role of Protein and Inhibitor Conformational Dynamics in the Reaction Mechanism

“…16 The value obtained for 11a is similar to those found for the formation of IP under the presence of other inhibitors: 7.3 kcal•mol -1 with an a-ketoamide inhibitor 40 and 10.3 with a Michael acceptor. 34 These value are systematically larger than the free energy cost evaluated for the apo enzyme, which was found to be 2.9 kcal•mol -1 in two different works, 16,40 indicating that desolvation of the active site upon ligand binding can destabilize the IP form. Diminution of this energy penalty through ligand design could be a promising strategy to improve inhibition binding and kinetics.…”